Without seeing more details, there are many possible reasons for the difference between your CLI results and the Classification Learner results. Here are some ideas:
(1) Are you using the same datasets for both? If you are only using a training set and a test set at the CLI, without cross-validation, then you should be sure to look at the test set accuracy within the Classification Learner app. To do that, load the training data into the classification Learner app, start the session with your choice of hold-out validation or cross-validation, then train your model, then load the test data, then look at the results on the test data (not the validation results).
(2) Are the fitcsvm training parameters the same at the CLI and in Classification Learner? Prior to model training, check the parameters within Classification Learner using the model summary tab.
For more detailed guidance, attached your data (or a subset thereof) and your corresponding results.
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